Yuzu (Citrus junos) is considered a health food in Japan, and the consumption is substantially increasing. However, after the juice is extracted from fruit, most of the peel is treated as waste. On the other hand, the number of Japanese Brown Cattle-Kochi, which is one domestic breed of Wagyu, has been reducing, therefore, the total number is only 1,700 at present. In this study, we evaluated the metabolomics of liver and skeletal muscle in Japanese Brown Cattle-Kochi after feeding yuzu peel, and examined whether yuzu peel altered the metabolism and added a high value to their beef. This experiments were conducted from September in 2015 to February in 2016. For analysis of metabolite in the liver, a total of 8 cattle (Yuzu feeding group: 4, non-feeding group: 4) were examined. Moreover, for analysis of metabolite in the skeletal muscle, 10 Japanese Brown Cattle (yuzu feeding group: 4, non-feeding group: 6), 3 Japanese Black Cattle, 3 beef from United States, and 3 beef from Australia were examined. Yuzu peel paste of 2.5% was added to feed for two weeks before slaughter. After slaughter, livers were collected immediately. Skeletal muscles were vacuum-packed and stored at 0°C for 20 days. The metabolites were analyzed by CE-TOFMS. In the liver, metabolites, which participate in deoxidization (e.g. glutathione, anserine, and carnosine), were increased in yuzu feeding group. In the skeletal muscle, there were huge differences of metabolites among four kinds of beef. The amounts of amino acid were higher in US and Australian beef than Wagyu beef. Yuzu feeding group contained more succnic acid, glutathione, and carnosine than another group. These results suggest that yuzu alter metabolism in the liver of Japanese Brown Cattle-Kochi, and add a high value to their beef.